Meeting 09.07.2014 - questions and notes

[alberskib]

Questions:

• Currently for GO we support: has part, part of, is a, regulates, negatively regulates, positively regulates what about others ie. occurs in
• aws console
• ncbiTaxonomy
• GoMapper, GoWriters (DI)
• compota - files handling, web interface?

[laughedelic]

wait, today is only 06.07.2014. are you from the future??? o_o

[alberskib]

Generally, I am preparing questions for nearest meeting - that's all. In other words: I am planning to ask this question in 09.07.2014 :) After meeting I will add notes.

[laughedelic]

Ah, ok ") sorry, I was a bit confused..

[laughedelic]

• first question to @eparejatobes and @pablopareja, why aren't there all relationships from GO?
• aws stuff is fixed: https://github.com/bio4j/dynamograph/issues/39
• ncbiTaxonomy model: https://github.com/bio4j/scala-model/blob/master/src/main/scala/bio4j/model/module/ncbiTaxonomy.scala
• writers/mappers implicit code refactoring recomendations: @laughedelic :facepunch: just do it!
• todo: move retries stuff from ServiceProvider to tabula

[pablopareja]

:question: :neutral_face: What question?

[alberskib]

Notes:

• I should concentrate on documentation - it is important !!!
• Distributed writng should be organized in some kind of streams - I should prepare some code and in case of any problems contact with @evdokim
• GoMapper/GoWriter could be refactored using implicits - I will receive instructions
• Next meeting is on Friday - it can change
• Throughput for tables - we need to define sufficient throughput values for GO tables (not so gigh, not so small)

[alberskib]

@pablopareja In Gene onthology there is also next type of relationship: occurs_in but in model this kind of relationship is not present - it is something deprecated?

[pablopareja]

Hey! I just downloaded and checked out the last version of the OBO-XML file and there's no hit for that relationship. Where did you get that relationship type from?

[alberskib]

When you open file: http://geneontology.org/ontology/go.obo and search relationship: occurs_in you will find ie. entry with GO:0000963 id that has this relationship declared in file

[pablopareja]

You're right but so far we've been using the OBO-XML format; http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz And there you cannot find any occurrence of that relationship... I have no idea why... One of them must be either wrong or outdated :confused:

[alberskib]

I also find occurs_in relationship in next file: http://purl.obolibrary.org/obo/go.owl. On next page http://www.geneontology.org/page/download-ontology OBO-XML is under legacy downloads section.

[eparejatobes]

@pablopareja @alberskib see Cross products in the GO docs. It's something that as far I know no tool relying on GO uses; kind of an experiment at this point.

[eparejatobes]

Also GO Ontology relations, this could be outdated though

[alberskib]

In the file http://purl.obolibrary.org/obo/go.owl. occurs_in can be found about 6 times in relationship tag and much more in intersection tag. To sum up which format is outdated?

[eparejatobes]

None of them :) it's the data. The standard GO distribution only considers the relations that we already have; all the others (like occurs_in) are part of the extended GO distribution.

[alberskib]

OK Great to know. Thanks